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- PDB-1mx8: Two homologous rat cellular retinol-binding proteins differ in lo... -

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Basic information

Entry
Database: PDB / ID: 1mx8
TitleTwo homologous rat cellular retinol-binding proteins differ in local structure and flexibility
ComponentsCELLULAR RETINOL-BINDING PROTEIN I, HOLO
KeywordsLIPID BINDING PROTEIN / beta-barrel / helix-turn-helix / vitamin A / Retonol binding / Transport
Function / homology
Function and homology information


regulation of granulocyte differentiation / response to benzoic acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / all-trans-retinol binding / retinoic acid biosynthetic process / maintenance of location in cell / vitamin A metabolic process / lipid storage / retinal binding ...regulation of granulocyte differentiation / response to benzoic acid / The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / all-trans-retinol binding / retinoic acid biosynthetic process / maintenance of location in cell / vitamin A metabolic process / lipid storage / retinal binding / response to vitamin A / retinoic acid metabolic process / retinol metabolic process / retinol binding / lipid homeostasis / response to retinoic acid / fatty acid transport / retinoid metabolic process / lipid droplet / fatty acid binding / cell body / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry simulated annealing
Model type detailsminimized average
AuthorsLu, J. / Cistola, D.P. / Li, E.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Two homologous rat cellular retinol-binding proteins differ in local conformational flexibility.
Authors: Lu, J. / Cistola, D.P. / Li, E.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics
Authors: Lu, J. / Lin, C.L. / Tang, C. / Ponder, J.W. / Kao, J.L. / Cistola, D.P. / Li, E.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure
Authors: Lu, J. / Lin, C.L. / Tang, C. / Ponder, J.W. / Kao, J.L.F. / Cistola, D.P. / Li, E.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding ...Title: Crystallographic studies on a family of cellular lipophilic transport proteins. Refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-binding protein in complex with all-trans-retinol
Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structures of holo and apo-cellular retinol-binding protein II
Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J.
#5: Journal: J.Biol.Chem. / Year: 2002
Title: Structure and backbone dynamics of apo- and holo-cellular retinal-binding protein in solution
Authors: Franzoni, L. / Lucke, C. / Perez, C. / Cavazzini, D. / Rademacher, M. / Ludwig, C. / Spisni, A. / Rossi, G.L. / Ruterjans, H.
History
DepositionOct 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULAR RETINOL-BINDING PROTEIN I, HOLO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0112
Polymers15,7251
Non-polymers2861
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein CELLULAR RETINOL-BINDING PROTEIN I, HOLO / Retinol binding protein -I (cellular) / CRBP


Mass: 15724.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RBP1 or RBP-1 / Plasmid: pMON CRBP I / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02696
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: Triple resonance experiments for the 1H, 15N and 13C resonance assignments included the following: HNCO CBCACONNH HNCACB CBCACOCAHA HCCH-TOCSY 15N-resolved TOCSY-HSQC; The intra-ligand NOE ...Text: Triple resonance experiments for the 1H, 15N and 13C resonance assignments included the following: HNCO CBCACONNH HNCACB CBCACOCAHA HCCH-TOCSY 15N-resolved TOCSY-HSQC; The intra-ligand NOE constraints as well as ligand-protein NOE constraints were obtained from 2D 13C and 15N double half-filtered experiment

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM cellular retinol-binding protein I U-[99% 15N, 99% 13C] in complex with all-trans retinol (natural isotope abundance); 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O95% H2O/5% D2O
21.0mM cellular retinol-binding protein I U-[99% 15N, 80% 2H] in complex with all-trans retinol (natural isotope abundance); 20mM phosphate buffer, 50mM potassium chloride, 0.05% sudium azide, 5mM beta-mecaptoethanol-d6; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.347.4ambient 298 K
20.346.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian UNITYPLUSVarianUNITYPLUS5003
Varian UNITYVarianUNITY6004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1varian associatescollection
VNMR6.1varian associatesprocessing
Felix2000molecular simulation inc.data analysis
Tinker3.3Ponder, J.W.structure solution
Tinker3.3Ponder, J.W.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 25

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